title: Analysis of protein-RNA complexes involving a RNA recognition motif engineered to bind hairpins with seven- and eight-nucleotide loops.
abstract: U1A binds U1hpII, a hairpin RNA with a 10-nucleotide loop. A U1A mutant (ΔK50ΔM51) binds U1hpII-derived hairpins with shorter loops, making it an interesting scaffold for engineering or evolving proteins that bind similarly sized disease-related hairpin RNAs. However, a more detailed understanding of complexes involving ΔK50ΔM51 is likely a prerequisite to generating such proteins. Toward this end, we measured mutational effects for complexes involving U1A ΔK50ΔM51 and U1hpII-derived hairpin RNAs with seven- or eight-nucleotide loops and identified contacts that are critical to the stabilization of these complexes. Our data provide valuable insight into sequence-selective recognition of seven- or eight-nucleotide loop hairpins by an engineered RNA binding protein.
authors.affiliation: Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, Colorado State University , Fort Collins, Colorado 80523, United States.
authors.forename: Brett D
authors.initials: BD
authors.lastname: Blakeley
authors.forename: Jenifer
authors.initials: J
authors.lastname: Shattuck
authors.forename: Melissa B
authors.initials: MB
authors.lastname: Coates
authors.forename: Evelyn
authors.initials: E
authors.lastname: Tran
authors.forename: Ite A
authors.initials: IA
authors.lastname: Laird-Offringa
authors.forename: Brian R
authors.initials: BR
authors.lastname: McNaughton
mesh_terms: D005454:Fluorescence Polarization; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA